Evolution of a Mitochondrial CytochromebGene Sequence in the Species-Rich GenusSebastes(Teleostei, Scorpaenidae) and Its Utility in Testing the Monophyly of the SubgenusSebastomus

The ecologically diverse and species-rich rockfishes (Sebastes) are a useful group for the study of marine speciation. The monophyly of the genus is generally accepted, as is the validity of most of the numerous species found along the West Coast of North America. However, the subgeneric groupings that would help in the proposal and interpretation of various speciation schemes are poorly supported based on widely overlapping morphological characters. The use of genetic characters provides an alternative approach. In this study, we present the first quantitative analysis supporting the monophyly of all 14 species of the subgenusSebastomusamong 54 congeners. The structural features and evolution of the 750 bp of the cytochromebgene used to test the monophyly were similar to those of other vertebrates. Low levels of intrageneric sequence divergence (<10%) and incipient levels of saturation at third-codon positions were found in the gene. The monophyly ofSebastomuswas supported in extensive phylogenetic analyses using distance, cladistic, and likelihood methods. Further corroboration was obtained from permutation- and simulation-based statistical tests.     

Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus) from the sky islands of the Rocky Mountains

Grasshoppers in the genus Melanoplus have undergone a radiation in the 'sky islands' of western North America, with many species originating during the Pleistocene. Despite their recent origins, phylogenetic analyses indicate that all the species exhibit monophyletic or paraphyletic gene trees. The objectives of this study were to determine whether the monophyletic genealogies are the result of a bottleneck at speciation and to investigate the extent to which the different phylogenetic states of eight species (i.e. monophyletic versus paraphyletic gene trees) can be ascribed to the effects of speciation. A coalescent simulation was used to test for a bottleneck at speciation in each species. The effective population sizes and demographic histories of species were compared across taxa to evaluate the possibility that the paraphyly versus monophyly of the species reflects differential rates of lineage loss rather than speciation mode. While coalescent analyses indicate that the monophyly of Melanoplus species might not be indicative of bottlenecks at speciation, the results suggest that the paraphyletic gene trees may reflect the demography of speciation, involving localized divergences in the ancestral species. With respect to different models of Pleistocene divergence, the data do not support a model of founder-effect speciation but are compatible with divergence in allopatric refugia.     

Phylogenetic analysis of the family Ariidae (Ostariophysi: Siluriformes), with a hypothesis on the monophyly and relationships of the genera

Ariid monophyly and intrafamilial relationships are investigated based on cladistic analysis of 230 morphological characters. Terminal taxa examined include whenever possible type‐species, or the most morphologically similar species to the type‐species of the nominal genera, and the largest possible number of species, including cleared and stained specimens, available in zoological collections. Previous hypotheses about monophyly of the Ariidae are strongly corroborated by new synapomorphies discovered in the present study. The subfamily Galeichthyinae and the remaining ariids are strongly supported by new morphological characters. The monotypic subfamily Bagreinae is recognized as the sister group to all nongaleichthyin ariids, supported by a large series of exclusive synapomorphies. A new concept of Ariinae is presented: the subfamily is found to be unequivocally monophyletic and includes all ariid genera, except Galeichthys and Bagre. New data supporting the monophyly of the genera included in the Ariinae are introduced and previous hypotheses of monophyly, species composition, morphological definition, and relationships are reviewed and discussed.     

Cryptic speciation on the high seas; global phylogenetics of the copepod family Eucalanidae

Few genetic data are currently available to assess patterns of population differentiation and speciation in planktonic taxa that inhabit the open ocean. A phylogenetic study of the oceanic copepod family Eucalanidae was undertaken to develop a model zooplankton taxon in which speciation events can be confidently identified. A global survey of 20 described species (526 individuals) sampled from 88 locations worldwide found high levels of cryptic diversity at the species level. Mitochondrial (16S rRNA, CO1) and nuclear (ITS2) DNA sequence data support 12 new genetic lineages as highly distinct from other populations with which they are currently considered conspecific. Out of these 12, at least four are new species. The circumglobal, boundary current species Rhincalanus nasutus was found to be a cryptic species complex, with genetic divergence between populations unrelated to geographic distance. 'Conspecific' populations of seven species exhibited varying levels of genetic differentiation between Atlantic and Pacific basins, suggesting that continental landmasses form barriers to dispersal for a subset of circumglobal species. A molecular phylogeny of the family based on both mitochondrial (16S rRNA) and nuclear (ITS2, 18S rRNA) gene loci supports monophyly of the family Eucalanidae, all four eucalanid genera and the 'pileatus' and 'subtenuis' species groups.     

Testing the monophyly of the New Zealand and Australian endemic family Conoesucidae Ross based on combined molecular and morphological data (Insecta: Trichoptera: Sericostomatoidea)

Conoesucidae (Trichoptera, Insecta) are restricted to SE Australia, Tasmania and New Zealand. The family includes 42 described species in 12 genera, and each genus is endemic to either New Zealand or Australia. Although monophyly has been previously assumed, no morphological characters have been proposed to represent synapomorphies for the group. We collected molecular data from two mitochondrial genes (16S and cytochrome oxidase I), one nuclear gene (elongation factor 1-α) (2237–2277 bp in total), and 12 morphological characters to produce the first phylogeny of the family. We combined the molecular and morphological characters and performed both a maximum parsimony analysis and a Bayesian analysis to test the monophyly of the family, and to hypothesize the phylogeny among its genera. The parsimony analysis revealed a single most parsimonious tree with Conoesucidae being a monophyletic taxon and sistergroup to the Calocidae. The Bayesian inference produced a distribution of trees, the consensus of which is supported with posterior probabilities of 100% for 15 out of 22 possible ingroup clades including the most basal branch of the family, indicating strong support for a monophyletic Conoesucidae. The most parsimonious tree and the tree from the Bayesian analysis were identical except that the ingroup genus Pycnocentria changed position by jumping to a neighbouring clade. Based on the assumption that the ancestral conoesucid species was present on both New Zealand and Australia, a biogeographical analysis using the dispersal-vicariance criteria demonstrated that one or two (depending on which of the two phylogenetic reconstructions were applied) sympatric speciation events took place on New Zealand prior to a single, late dispersal from New Zealand to Australia.     

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.     

Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax)

Many studies of phylogeography, speciation, and species limits restrict their focus to a narrow issue: gene tree monophyly. However, reciprocal monophyly does not provide an ideal touchstone criterion of any aspect of evolutionary divergence. There is a continuum of divergence stages as isolated populations go from initial allele frequency differences to well-differentiated species. Studying intermediate stages of divergence will increase our understanding of geographical speciation, species limits, and conservation priorities. We develop a conceptual framework and terminology for thinking about the stages of 'intermediate polyphyly'. The Holarctic clade of common ravens (Corvus corax), found throughout much of Eurasia and North America, provides a case study of these stages of intermediate divergence. We used coalescent, phylogenetic, and population genetic methods to investigate the history and current status of this Old World-New World distribution using 107 mitochondrial control region sequences. Phylogenetically, New World and Old World samples are intermixed. However, most samples are grouped into small subclades that are restricted to either the New World or the Old World, and only one haplotype is shared between the hemispheres. Analysis of moleculalr variance (amova) results reflect this low haplotype sharing between hemispheres (Phi(ST) = 0.13, P < 0.01). Isolation with Migration (im) coalescent results suggest a sustained period of divergence between the hemispheres and low levels of maternal gene flow. Although there has not been sufficient time to evolve reciprocal monophyly and some gene flow may occur, New World and Old World ravens are genetically quite distinct. We use this example to demonstrate these early stages of divergence as populations go from sharing only internal haplotypes, to sharing no haplotypes, to having population specific subclades. Studies of phylogeography, speciation and systematics will benefit from increased attention to these stages of intermediate polyphyly.     

Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

The genus Ixchela Huber is composed of 20 species distributed from north‐eastern Mexico to Central America, including the five new species described here from Mexico: I xchela azteca sp. nov. , I xchela jalisco sp. nov. , I xchela mendozai sp. nov. , I xchela purepecha sp. nov. and I xchela tlayuda sp. nov. We test the monophyly and investigate the phylogenetic relationships among species of the genus Ixchela using morphological and molecular data. Parsimony (PA) analysis of 24 taxa and 40 morphological characters with equal and implied weights supported the monophyly of Ixchela with eight morphological synapomorphies. The PA analyses with equal and implied weights, and separate Bayesian inference (BI) analyses for the CO1 gene (506 characters), concatenated gene fragments CO1 + 16S (885 characters), morphology + CO1 (546 characters) and the combined evidence data set (morphology + CO1 + 16S) (925 characters) support the monophyly of Ixchela. Our preferred topology shows two large clades; clade 1 has a natural distribution in the Mesoamerican biotic component, whereas clade 2 predominates in the Mexican Montane biotic component. The genus Ixchela diverged in the late Miocene, and the divergence between the internal clades in the genus occurred in the late Pliocene; by contrast, most of the speciation events seem to have occurred mainly during the Pleistocene, where climatic changes brought on by repeated glaciations played an important role in the diversification of the genus. © 2015 The Linnean Society of London     

Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena)

Recent speciation events provide important insights into the understanding and conservation of Earth's biodiversity, representing recent adaptations to a changing environment and an important source of future evolutionary potential. However, the most frequently applied criterion for molecular-based speciation investigations, that of reciprocal monophyly of mitochondrial sequences, overlooks recent speciation events where insufficient time has passed for fixed molecular differences to develop between putative species. Two morphologically distinguishable forms of finless porpoise (genus Neophocaena) exist in sympatry in the strait of Taiwan, however the taxonomic relationship of these different forms is controversial. To test the hypothesis that the two forms represent different species, a study was conducted based on morphological characters and microsatellite and mitochondrial markers. The data suggest that the two forms are highly differentiated in terms of both morphology and genetic characteristics, despite being sympatric, and therefore represent different species as defined by the biological species concept. Moreover, the two forms appear to have been reproductively isolated since sharing a common ancestor prior to the last major glaciation event approximately 18 000 years ago. However, this represents an insufficient amount of time for reciprocal monophyly to have developed, and thus previous studies based on this criterion have overlooked this speciation event and resulted in incorrect taxonomic classification of these forms.     

Cladistic analysis and osteological descriptions of the frog species in the Leptodactylus fuscus species group (Anura, Leptodactylidae)

The genus Leptodactylus is predominantly Neotropical (a few species have colonized the southern Neartic region) and is distributed from Texas to Argentina and on certain Caribbean islands. Leptodactylus was divided into five groups of species: Leptodactylus melanonotus , Leptodactylus ocellatus, Leptodactylus fuscus , Leptodactylus pentadactylus and Leptodactylus marmoratus . Among these, the L. fuscus group is the one with most species, with 27 taxa. Characters unverified in most of the species are used to define the L. fuscus group. However, the monophyly of the group has never been tested rigorously in a quantitative phylogenetic context. Thus, the main goal of this study was to test such monophyly and to construct a phylogeny of the L. fuscus group. A matrix of 114 characters scored across 43 taxa was constructed, with 31 characters taken from external morphology, 58 from adult skeletons, 16 from larval chondrocranium, 5 from ethology and 4 from morphometric data were included. Out of all the species examined, 23 belonged to the ingroup and 20 to the outgroup. The data set was analysed with implied weights, by using TNT software. The monophyly of the group was strongly supported in the fittest cladogram obtained. The optimizations of some characters on this hypothesis support traditional evolutionary hypotheses. The optimizations also suggest the presence of paedomorphic character states in some species, which is also discussed.     

Geographical versus ecological isolation of closely related black flies (Diptera: Simuliidae) inferred from phylogeny, geography, and ecology

To investigate patterns of geographical and ecological separation among morphologically similar, closely related species of black flies, we integrated ecological, geographical, and phylogenetic information, based on multiple gene sequences, for 12 species in the subgenus Gomphostilbia in Thailand. Molecular characters supported the monophyly of the Simulium ceylonicum species group, but not of the Simulium batoense species group, suggesting that revisionary work is needed for the latter. Both ecological and geographical isolation of similar taxa were revealed. Stream velocity and altitude were among the principal ecological factors differing between closely related species. Most closely related species in the subgenus Gomphostilbia overlap geographically, suggesting the possibility of sympatric speciation driven by ecological divergence. Geographical isolation via dispersal also might have contributed to species divergence, while Pleistocene climate changes possibly influenced population genetic structure, demographic history, and speciation of some members of the subgenus.     

Phylogeny of nereidids (Polychaeta, Nereididae) with paragnaths

A phylogenetic analysis was conducted of the Nereidinae — those members of the Nereididae (Polychaeta) with pharyngeal paragnaths. We had two objectives: to test the monophyly of currently accepted genera, subgenera and informal subgeneric groupings within the Nereidinae, and, if warranted, to propose a more natural classification of the Nereidinae. Parsimony analyses were undertaken, including 52 terminal taxa from all genera and informal groupings from the large heterogeneous genera Nereis , Ceratonereis , Neanthes and Perinereis . Analyses of a character set of 52 informative characters yielded more than 10 000 equally parsimonious trees with a length of 176 steps (consistency index [CI] = 0.34, retention index [RI] = 0.66). Reweighting three times resulted in 445 most parsimonious trees with length 54.62 (CI = 0.59, RI = 0.79). Many characters widely used in nereidid systematics were found to exhibit high levels of homoplasy. The most parsimonious trees could not be rooted such that the selected ingroup, 'Nereididae with paragnaths', was monophyletic, causing us to reject the monophyly of the Nereidinae as currently defined. The following genera were well supported by the parsimony analyses and are newly diagnosed: Alitta , Ceratonereis , Pseudonereis , Simplisetia , Solomononereis and Unanereis . Alitta succinea , Pseudonereis cortezi , Pseudonereis noodti and Pseudonereis pseudonoodti are proposed as new combinations. The parsimony analysis supported the monophyly of neither Composetia , Neanthes , Nereis and Perinereis nor of any new groupings of remaining species presently placed in those genera. It is these poorly supported genera that comprise most species of Nereididae.     

The geometry of the marmot (rodentia: sciuridae) mandible: phylogeny and patterns of morphological evolution

Marmots have a prominent role in the study of mammalian social evolution, but only recently has their systematics received the attention it deserves if sociobiological studies are to be placed in a phylogenetic context. Sciurid morphology can be used as model to test the congruence between morphological change and phylogeny because sciurid skeletal characters are considered to be inclined to convergence. However, no morphological study involving all marmot species has ever been undertaken. Geometric morphometric techniques were applied in a comparative study of the marmot mandible. The adults of all 14 living marmot species were compared, and mean mandible shape were used to investigate morphological evolution in the genus Marmota. Three major trends were observed. First, the phylogenetic signal in the variation of landmark geometry, which describes mandible morphology, seems to account for the shape differences at intermediate taxonomic levels. The subgenera Marmota and Petromarmota, recently proposed on the basis of mitochondrial cytochrome b sequence, receive support from mandible morphology. When other sciurid genera were included in the analysis, the monophyly of the genus Marmota and that of the tribe Marmotini (i.e., marmots, prairie dogs, and ground squirrels) was strengthened by the morphological data. Second, the marmotine mandible may have evolved as a mosaic of characters and does not show convergence determined by size similarities. Third, allopatric speciation in peripheral isolates may have acted as a powerful force for modeling shape. This hypothesis is strongly supported by the peculiar mandible of M. vancouverensis and, to a lesser degree, by that of M. olympus, both thought to have originated as isolated populations in Pleistocene ice-free refugia.     

Anatomy and phylogenetic analysis of the neotropical callichthyid catfishes (Ostariophysi, Siluriformes)

Based mainly on morphological characters, the phylogenetic relationships among genera and some species groups of the neotropical family Callichthyidae were examined. A study of the osteology of a generalized callichthyid, Callichthys callichthys (Linnaeus), with detailed comparisons among representatives of the remaining genera in the family, is presented and used as a basis for the phylogenetic analysis. A single most parsimonious tree supported the monophyly of the family Callichthyidae based on 28 derived features and the division of the family in the subfamilies Corydoradinae and Callichthyinae. In the subfamily Corydoradinae, the genus Aspidoras is the sister-group of the clade formed by Corydoras plus Brochis. Five derived features support the monophyly of this clade and four support the monophyly of Brochis. No characters, however, were found to support the genus Corydoras. In the subfamily Callichthyinae, Dianema and Hopbstemum are sister-taxa. Megalechis represents the sister-group of Dianema plus Hoplosternum and Lepthoplosternum represents the sister-group to Megalechis plus Dianema plus Hopbstemum. Finally, Callichthys is considered the least derived member of the subfamily, and is hypothesized as the sister-group of the remaining species. A key to all callichthyid genera is provided.     

Limited role of character displacement in the coexistence of congeneric Anelosimus spiders in a Madagascan montane forest

Evolutionary and ecological theory predicts that closely related and similar species should coexist infrequently because speciation is more likely to occur allopatrically than sympatrically, and because co‐occurring species with similar traits may compete for limited resources, leading to competitive exclusion or character displacement. Here we study the unusual coexistence of 10 similar congeneric species of Anelosimus spiders within a small forest fragment in Madagascar. We asked if these species radiated in sympatry or allopatry, and if there was evidence for local‐scale character displacement in body size and other species‐level traits. We sampled ～ 350 colonies (6346 individuals) along a 2800 m transect. We identified colonies using morphology and DNA barcoding, and tested the monophyly of local and regional species assemblages with time‐calibrated phylogenies. We used null model analysis and phylogenetic signal inference to test for patterns of segregation in body size, microhabitat, phenology, and seasonality of coexisting species. We found that all species belong to a Madagascan clade that radiated during the Pliocene, but that contemporary local assemblages are non‐monophyletic. This is consistent with allopatric speciation during periods of global cooling and expansion of grasslands, and subsequent species assembly as forest fragments re‐expanded and coalesced. We found no evidence for character displacement, except for overdispersion and even spacing in phenology: species were segregated by instars in a manner consistent with resource partitioning or maintenance of reproductive isolation. Overdispersion or even spacing in phenology may contribute to coexistence either through resource partitioning or mate recognition. However, there was no support for a scenario of resource partitioning and divergence of body size or other correlated morphological characters. These traits are better explained by evolutionary forces operating during speciation, rather than ecological forces operating during local community assembly.     

Molecular systematics in Aratinga parakeets: species limits and historical biogeography in the 'solstitialis' group, and the systematic position of Nandayus nenday

The parrot genus Aratinga comprises 20 species that can be separated, based on morphological characters, in at least three distinct groups. We performed a phylogenetic analysis based on mtDNA sequences of individuals belonging to the solstitialis group with the objectives of: (1) assessing the genetic differences among individuals in order to clarify their specific status; (2) testing the monophyly of the group and establishing its phylogenetic position relative to other Aratinga species, (3) making inferences about temporal and geographical patterns of diversification in the Neotropics. As a result of the analysis, the three taxa belonging to the Aratinga solstitialis complex were found to be diagnosable phylogenetic species, the monotypic genus Nandayus was found to be included in the solstitialis group and the non-monophyly of the genus Aratinga was confirmed. Most of the speciation events occurred during the Pliocene and Pleistocene and may be related to habitat shifts associated to climate oscillation during these periods.     

Phylogenetic relationships,subdivision, and biogeography of the cyprinid tribe Labeonini (sensu ) (Teleostei: Cypriniformes), with comments on the implications of lips and associated structures in the labeonin classification

The Labeonini (sensu Rainboth, 1991) is a tribe of the subfamily Cyprininae, the largest subfamily of Cypriniformes. With around 400 species in 34 genera, this tribe is widely distributed in the freshwaters of tropical Africa and Asia. Most species are adapted to fast-flowing streams and rivers, and exhibit unique morphological modifications associated with their lips and other structures around the mouth. The monophyly of this tribe has been tested and generally accepted in previous morphological and molecular studies. The major objectives of this study were to reconstruct the phylogenetic relationships within the tribe Labeonini, test its monophyly and explore the taxonomic subdivisions, intrarelationships and biogeography of the group. The value of the morphological characters associated with the lips and other associated structures in the taxonomic classification of labeonins was also discussed. Nucleotide sequences (3867 bp) of four unlinked nuclear loci were obtained from 51 species in 18 Labeonini genera from throughout the range of the tribe. Maximum parsimony, partitioned maximum likelihood and partitioned Bayesian analyses were used for phylogenetic inference from combined and separate gene data sets. Based on our results, the monophyly of Labeonini was well supported. Two major clades could be recovered within the tribe. Three subclades could further be recognized from the first clade. These clades/subclades are not consistent with groupings of any of previous workers using either morphological or molecular characters for phylogenetic inference. Only five currently recognized genera in this analysis are monophyletic. The similarity between some lips and associated structures (e.g. suctorial discs) of labeonins may due to convergence or parallelism instead of common ancestry. Labeonins of Southeast Asia, India and China are closely related to each other; the multiple clades of African taxa do not form a single monophyletic group, indicating multiple, independent dispersal events of labeonins into Africa from Asia.     

Nuclear gene genealogies reveal historical,demographic and selective factors associated with speciation in field crickets

Population genetics theory predicts that genetic drift should eliminate shared polymorphism, leading to monophyly or exclusivity of populations, when the elapsed time between lineage-splitting events is large relative to effective population size. We examined patterns of nucleotide variation in introns at four nuclear loci to relate processes affecting the history of genes to patterns of divergence among natural populations and species. Ancestral polymorphisms were shared among three recognized species, Gryllus firmus, G. pennsylvanicus, and G. ovisopis, and genealogical patterns suggest that successive speciation events occurred recently and rapidly relative to effective population size. High levels of shared polymorphism among these morphologically, behaviorally, and ecologically distinct species indicate that only a small fraction of the genome needs to become differentiated for speciation to occur. Among the four nuclear gene loci there was a 10-fold range in nucleotide diversity, and patterns of polymorphism and divergence suggest that natural selection has acted to maintain or eliminate variation at some loci. While nuclear gene genealogies may have limited applications in phylogeography or other approaches dependent on population monophyly, they provide important insights into the historical, demographic, and selective forces that shape speciation.